Search Results for "samtools"
Sort By:
Showing 9 open source projects for "samtools"
View related business solutions-
Ship Agents FasterGemini Enterprise Agent Platform lets you rapidly build, scale, govern and optimize production-ready agents grounded in your organization's data. The platform enables developers to build custom or pre-built agents for virtually any use case. New customers get $300 in free credits.
-
Custom VMs From 1 to 96 vCPUs With 99.95% UptimeLive migration and automatic failover keep workloads online through maintenance. One free e2-micro VM every month.
-
1
TARGT pipeline
Targeted Analysis of sequence Reads for GenoTyping of HLA/MHC genes
...The pipeline consists of a main bash script that calls the different steps of the pipeline and can either be called directly or submitted to a cluster queue system, as well as additional sub-scripts and files, that are required to perform the different steps. The pipeline also requires installed versions of the mapping tool Bowtie2 and samtools. -
2
fusion-test
Script for fusion detection in DNAseq and RNAseq
...It uses chimerascan, SOAPfuse, MapSplice2, FusionMap, fusioncatcher, TopHat and EricScript. The output files of chimerascan are further annotated by Jinja and Pegasus Fusion. ***Updated*** Note: EricScript uses old version of Samtools. Download the modified program and Samtools-0.1.19 here. An error in the configuration for fusioncathcer is corrected. FusionMap has been deprecated. It is changed to Oshell. The old FusionMap is moved to fusionmap.sh. MapSplice is updated to 2.2.2. -
3
YFitter
Fitting Y chromosome haplogroups by maximum likelihood
Yfitter is a program for assigning Y chromosome haplogroups to individuals sequenced at low coverage. It is designed to be used in a samtools/bcftools pipeline. Yfitter also supports haplogrouping using chip genotype data. -
4
VarScan
Variant detection in next-generation sequencing data
Variant detection in massively parallel sequencing. For one sample, calls SNPs, indels, and consensus genotypes. For tumor-normal pairs, further classifies each variant as Germline, Somatic, or LOH, and also detects somatic copy number changes. THE LATEST VERSION IS AVAILABLE ON GITHUB -
Veeam Data Platform v13.1Try Veeam Data Platform today. Experience the unified platform that's secure by design, portable by default, and proven to recover clean, fast, and anywhere.
-
5
Hadoop-BAM is a Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework with the Picard SAM JDK, and command line tools similar to SAMtools. The file formats currently supported are BAM, SAM, FASTQ, FASTA, QSEQ, BCF, and VCF. For a longer high-level description of Hadoop-BAM, refer to the article "Hadoop-BAM: directly manipulating next generation sequencing data in the cloud" in Bioinformatics Volume 28 Issue 6 pp. 876-877, available online at: http://dx.doi.org/10.1093/bioinformatics/bts054 Note that the library part of Hadoop-BAM is mainly for developers with experience in using Hadoop. ...
-
6
AFSM_seq
a simple and rapid method for genome-wide SNP and methylation site
...Classified paired-ends using fltfastq2pe.pl. to produce output “R1.trim.pair.fastq” and “R2.trim.pair.fastq”. 4.The filtered sequence reads were aligned to the reference genome using the Bowtie2, allowing a maximum of four mismatches and one gap of up to 3 bp. Using the SAMtools pileup command the variable positions (SNPs) were determined. 5.AFSM_meth_V_1.0.pl are used for analyses of AFSM methylation results were based on comparisons of assembled sequences . perl AFSM_meth_V_1.0.pl -i output.sort.bam -o output.meth.matrix -
7
SOAPindel2
SOAPindel2 focusing on calling indels from the next-generation p
...The files with read-alignments. SOAPindel2 accepts only Indexed BAM formats as input. Users can use the tools/soap2sam.cc to convert SOAP format to SAM format and use samtools convert SAM to indexed BAM. SOAPindel2 can guess the library insert sizes by itself. Sequencing platform:Theoretically, SOAPindel2 is designed for all paired-end sequencing data because it doesn’t consider any qualities for now. So it works for both Ilumina GA data and 454 data, but we’ve only tested it on Ilumina GA data. -
8
vcf2MSAT
Find Microsatellites in a ".vcf" report
vcf2MSAT is a python program to identify microsatellite repeat regions based on known polymorphisms identified in a ".vcf" report after using SAMtools to analyze next-generation sequencing files. -
9
BCP
NGS analysis tool
BCP is a command-line tool ideated to analyze NGS data, also offering a wrapper for some common NGS software, including Fastx and Samtools. It is oriented mainly towards targeted resequencing experiments, with a set of functions for general purposes. BCP also includes a function for breast cancer risk estimation, based on the Gail model, using both clinical and genome data. -
$300 Free Credits to Build on Google CloudPut your $300 in credit toward real workloads, then keep building with free monthly usage for 20+ products. No commitment and no charge until you upgrade.
- Previous
- You're on page 1
- Next
